Annotation of org.Pf.plasmo.db out of date.
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@lucasmichel-20031
Last seen 5.2 years ago

The annotation in the package seems out of date.

The command org.Pf.plasmo_dbInfo() shows that the plasmo.db release used is 28 while the current release is 41. I am not sure where should I ask if there is the possibility to update it.

Thank you very much,

Lucas

org.Pf.plasmo.db • 686 views
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@james-w-macdonald-5106
Last seen 4 hours ago
United States

Non-model organisms like this are hard to get updated - we have limited resources as it is - so you would be better off building your own. I did this on Windows, so the call to install.packages requires a source=TRUE.

> library(AnnotationForge)
> makeOrgPackageFromNCBI("0.0.1","me <me@mine.org>","me", tax_id="36329", genus="Plasmodium",species="falciparum.3d7")
If files are not cached locally this may take awhile to assemble a 12 GB cache databse in the NCBIFilesDir directory. Subsequent calls to this function should be faster (seconds). The cache will try to rebuild once per day.
preparing data from NCBI ...
starting download for 
[1] gene2pubmed.gz
[2] gene2accession.gz
[3] gene2refseq.gz
[4] gene_info.gz
[5] gene2go.gz
getting data for gene2pubmed.gz
extracting data for our organism from : gene2pubmed
getting data for gene2accession.gz
extracting data for our organism from : gene2accession
getting data for gene2refseq.gz
extracting data for our organism from : gene2refseq
getting data for gene_info.gz
extracting data for our organism from : gene_info
getting data for gene2go.gz
extracting data for our organism from : gene2go
processing gene2pubmed
processing gene_info: chromosomes
processing gene_info: description
processing alias data
processing refseq data
processing accession data
processing GO data
Please be patient while we work out which organisms can be annotated
  with ensembl IDs.
making the OrgDb package ...
Populating genes table:
genes table filled
Populating pubmed table:
pubmed table filled
Populating chromosomes table:
chromosomes table filled
Populating gene_info table:
gene_info table filled
Populating entrez_genes table:
entrez_genes table filled
Populating alias table:
alias table filled
Populating refseq table:
refseq table filled
Populating accessions table:
accessions table filled
Populating go table:
go table filled
table metadata filled

'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
'select()' returned many:1 mapping between keys and columns
Populating go_all table:
go_all table filled
Creating package in c:/Users/jmacdon/Desktop/org.Pfalciparum.3d7.eg.db 

> install.packages("org.Pfalciparum.3d7.eg.db/", type = "source", repo=NULL)
Installing package into 'C:/Users/jmacdon/AppData/Roaming/R/win-library/3.5'
(as 'lib' is unspecified)
* installing *source* package 'org.Pfalciparum.3d7.eg.db' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'org.Pfalciparum.3d7.eg.db'
    finding HTML links ... done
    org.Pfalciparum 3d7.egBASE              html  
    org.Pfalciparum 3d7.egORGANISM          html  
    org.Pfalciparum 3d7.eg_dbconn           html  
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (org.Pfalciparum.3d7.eg.db)
In R CMD INSTALL
> 
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Thank you very much for the reply! I'll to do it myself then.

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Hi, I'm currently trying to built my own updated org.Pf.plasmo.db annotation package using makeOrgPackageFromNCBI() as described in James W. MacDonald's answer above. Unfortunately, I keep receiving error messages and the final package fails building. All my troubleshooting attempts have failed so far and I wonder if this is a general problem that others may currently also experience? I'd appreciate any comments how it currently works for you. Many thanks in advance!

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Please don't just append to a year old post. Make a new one. And you need to show code. Just saying that something happened isn't the same as showing what happened.

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